Claude Skills by HolobiomicsLab

Use when you have an LC-MS peak-intensity matrix (rows = peaks with m/z

Use when after loading MS-Dial feature tables (e.g., Urine_RP_NEG_norm.txt

Use when you have centroided data-dependent acquisition (DDA) mzML files

Use when extracting migration times of specific analyte or reference

Use when you have statistically significant LC-MS features and need to

Use when when linking statistically significant LC-MS features into structural

Use when when you have observed fragment peak m/z values from tandem

Use when you have an MS/MS spectrum with observed peaks and a peptidoform

Use when you have experimental peak lists (m/z, retention time, intensity)

Use when when converting raw line-scan mass spectrometry imaging data

Use when when implementing adduct detection in LC-MS metabolomics workflows,

Use when after calculating neutral mass from observed m/z and adduct

Use when your pandas DataFrame contains mass spectrometry data with retention

Use when after constructing initial data bins from mzTree (indexed by

Use when after mass tracks have been aligned across all samples (either

Use when when you have centroided mzML files from LC-MS metabolomics

Use when after constructing a LOWESS regression function (rt_cal_dict)

'Use when when you have centroid mzML files from LC-MS metabolomics acquisition

Use when after discovering Mass2Motifs through LDA topic modeling of

Use when after LDA-based Mass2Motif discovery has generated a set of

Use when after MS2LDA has inferred a motifset and you need to visualize

Use when when you have a preprocessed bag-of-fragments corpus from tandem

Use when when you have preprocessed MS/MS spectra converted to a bag-of-fragments

Use when you have created a GNPS molecular network (classical or feature-based

Use when you have a collection of MassBank records (in plain-text or

'Use when after individual mass tracks (EICs) have been extracted from

Use when you have trained a shallow decision tree on ChemEcho feature

Use when you need to search for specific mass spectrometry patterns (e.g.,

Use when you have completed one or more domain-specific MASST searches

Use when you need to run the Zamboni-lab Masster (MASSter) workflow for

Use when you have a GC-MS dataset with Match.Factor scores for each detected

Use when you have multiple CDF files containing mass spectrometry imaging

Use when you have two separate LC-MS untargeted metabolomic feature datasets

Use when you have mass spectrometry data in mzXML or mzML format and

Use when you have located MATLAB scripts in a Codes-Explained folder

Use when when you have mass spectrometry imaging root datasets paired

Use when when you have mass spectrometry data (chromatograms, spectra,

'Use when when rendering spectrum data (m/z vs. intensity arrays) from

Use when when you have a confusion matrix (predicted vs. ground-truth

Use when you have mass spectrometry data in a pandas DataFrame with retention

Use when you have normalized and standardized metabolomics data (samples

Use when after feature filtering has removed low-abundance or highly

Use when you have IC-FTMS measurement records in JSON format with multiple

Use when you have extracted tabular data in intermediate JSON form and

Use when after rMSIcleanup has classified ions as matrix-related or non-matrix,

Use when after completing 10-fold cross-validated training of MiMeNet

Use when after computing a Jacobian (precision) matrix from covariance

Use when after executing memo_from_unaligned or memo_from_aligned functions

Use when when you need to subset a backend containing multiple MS spectra

Use when preparing a software release and you need to verify that all